tools issueshttps://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues2024-03-13T10:53:32Zhttps://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/57FROGS : Phyloseq_beta_diversity : Outputs non disponibles2024-03-13T10:53:32ZVincent DarbotFROGS : Phyloseq_beta_diversity : Outputs non disponiblesBonjour,
Lorsque nous lançons l'outil phyloseq_beta_diversity de FROGS, bien que l'outil fonctionne et que le html sorte correctement, les fichiers .tsv ne sont pas sorties dans les outputs Galaxy (bien que les matrices soient correctem...Bonjour,
Lorsque nous lançons l'outil phyloseq_beta_diversity de FROGS, bien que l'outil fonctionne et que le html sorte correctement, les fichiers .tsv ne sont pas sorties dans les outputs Galaxy (bien que les matrices soient correctement calculés lors du lancement de l'outil).
La particularité est que ces .tsv peuvent être 1 ou plusieurs, pour cela nous avons donc utilisé cette balise dans le code xml qui permet d'automatiquement identifier le nombre de sorties tsv :
<discover_datasets pattern="__designation__" ext="tsv" directory="BetaMatrix" visible="true"/>
J'ai testé l'outil sur une instance galaxy en local de même version que celle sur l'IFB (23.1.5), et l'outil est lancé normlement. Avez-vous une idée d'où peut provenir ce problème ?
Merci d'avance pour votre aide
Cordialement,
Vincent Darbothttps://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/56Tools update: don't fail if no update2024-01-29T09:08:49ZAnthony BretaudeauTools update: don't fail if no updatehttps://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/55Tools install playbook ignore errors2024-01-29T09:08:12ZAnthony BretaudeauTools install playbook ignore errorsThis install job should have detected the failure: https://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/jobs/6025167850This install job should have detected the failure: https://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/jobs/6025167850https://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/54Database name problem2024-01-25T09:35:43ZpimarinDatabase name problemHello,
I'm trying to submit workflow to the IWC standard publication, but some problem happened due to the database used in tool.
The problem is to use workflow in automatic way, you need to give the database name as a string input, bu...Hello,
I'm trying to submit workflow to the IWC standard publication, but some problem happened due to the database used in tool.
The problem is to use workflow in automatic way, you need to give the database name as a string input, but in the case of Kraken2 and bracken tools, which need to use the same database (this is a tool suite), the name stored by galaxy is different.
The name to give to kraken is :`2023-08-24T153645Z_standard_prebuilt_pluspf_16gb_2022-06-07` but the name to the same database into bracken tool is :`41c59a90-3759-486c-b865-bcffc966adde`
I think you need to sanitize the name of stored database and maybe have the same nomenclature between databaseAnthony BretaudeauAnthony Bretaudeauhttps://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/53Failed last abromics installation from the last MR2024-01-25T10:37:05ZpimarinFailed last abromics installation from the last MRThe [MR76](https://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/merge_requests/576) installed the last version of abromics 0.8.3.4 but don't uper in tool panel for the users...
The MR seem to be valid.The [MR76](https://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/merge_requests/576) installed the last version of abromics 0.8.3.4 but don't uper in tool panel for the users...
The MR seem to be valid.Anthony BretaudeauAnthony Bretaudeauhttps://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/49Problem with FROGS : FROGSFUNC_2_functions galaxy pannel2024-02-14T10:21:54ZVincent DarbotProblem with FROGS : FROGSFUNC_2_functions galaxy pannelHello,
There is a problem with a galaxy pannel for FROGS_2_function tool.
In the xml file, I have a parameter defined as follows and which refers to an associated .loc file:
```
<param argument="--functions" type="select" label="Targ...Hello,
There is a problem with a galaxy pannel for FROGS_2_function tool.
In the xml file, I have a parameter defined as follows and which refers to an associated .loc file:
```
<param argument="--functions" type="select" label="Target function database" multiple="true" optional="false" help=" 16S : at least 'EC' or/and 'KO' should be chosen (EC for Metacyc pathway analysis or/and KO for KEGG pathway analysis) - others values are optionnal. ITS and 18S : 'EC' only available." >
<options from_data_table="frogs_picrust2_functions">
<column name='name' index='1' />
<column name='value' index='1' />
<column name='path' index='2' />
<column name='traits' index='3' />
<filter type="param_value" ref="category" column="0" />
<validator type="expression" message="'EC' is the default database used by PICRUSt2. 'EC' or 'KO' must be at least selected. Other tables are optionnal">"EC" in value or "KO" in value</validator>
</options>
</param>
```
In the validator : `<validator type="expression" message="'EC' is the default database used by PICRUSt2. 'EC' or 'KO' must be at least selected. Other tables are optionnal">"EC" in value or "KO" in value</validator>`
I want EC or KO to be at least selected by the user : `"EC" in value or "KO" in value`
But when I chose an optionnal value, I can't launch the tool even though EC or KO is selected:
![pannel_problem](/uploads/0fd5cb4c4eee51dc860de635fcd66879/pannel_problem.png)
I tried to reproduce the error with my local galaxy machine (version 21.05), but there was no problem.
Do you have any idea where this might be coming from? Does the validator no longer work with more recent galaxy versions? (ifb galaxy is under version 23.07)
Thank you for your help
Regards,
Vincent DarbotRliboubanRliboubanhttps://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/45remove sra_pileup2023-11-15T10:19:50ZThomas Chaussepiedremove sra_pileupGalaxy tool error report from d********@************.fr (sra_pileup)Galaxy tool error report from d********@************.fr (sra_pileup)Thomas ChaussepiedThomas Chaussepiedhttps://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/40met4j tool with bad name2023-10-11T09:27:49ZAnthony Bretaudeaumet4j tool with bad nameThis is ugly:
![image](/uploads/a93c8638cdfb7d2e93fea85fc22fd4a1/image.png)This is ugly:
![image](/uploads/a93c8638cdfb7d2e93fea85fc22fd4a1/image.png)https://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/24Pycoqc No index found for bam file2023-10-11T09:26:29ZThomas ChaussepiedPycoqc No index found for bam filehttps://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/20Orders of labels/sections in tool_conf.xml is ignored2024-01-29T09:09:54ZAnthony BretaudeauOrders of labels/sections in tool_conf.xml is ignoredThe "species abundance" section should be [under the Galaxy-e label](https://gitlab.com/ifb-elixirfr/usegalaxy-fr/infrastructure/-/blob/preprod/templates/galaxy/tool_conf.xml#L218), instead of "Miscellaneous Tools"
The "Interactive tool...The "species abundance" section should be [under the Galaxy-e label](https://gitlab.com/ifb-elixirfr/usegalaxy-fr/infrastructure/-/blob/preprod/templates/galaxy/tool_conf.xml#L218), instead of "Miscellaneous Tools"
The "Interactive tools - metabolomics" should be under workflow4metabolomics, but it's not.
That's because the sort script doesn't even open tool_conf.xml, so it's not aware of these sections/labels orderinghttps://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/11Harmonize tool categories with usegalaxy.*2022-06-15T10:00:41ZAnthony BretaudeauHarmonize tool categories with usegalaxy.*https://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/10Auto install(some) tools from usegalaxy.*2022-06-15T10:00:32ZAnthony BretaudeauAuto install(some) tools from usegalaxy.*https://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools/-/issues/4run galaxy tools with singularity/pulsar embedded2022-06-15T10:00:30ZDavid Christianyrun galaxy tools with singularity/pulsar embeddedtest a tool using singularity instead of a conda environment.test a tool using singularity instead of a conda environment.